problem in installing abinit-6.2.2
Posted: Fri Dec 24, 2010 7:41 pm
dear,
when i try to install abinit-6.2.2 in parallel configuration i got following message.could some one tell me what went wrong?
when i try to install abinit-6.2.2 in parallel configuration i got following message.could some one tell me what went wrong?
Code: Select all
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking which type of compiler we have... gnu 4.4
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether byte ordering is bigendian... no
==============================================================================
=== C++ support ===
==============================================================================
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking which type of C++ compiler we have... gnu 4.4
==============================================================================
=== Fortran support ===
==============================================================================
checking whether we are using the GNU Fortran compiler... no
checking whether /home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort accepts -g... yes
checking which type of Fortran compiler we have... intel 11.1
checking fortran 90 modules extension... mod
checking for Fortran flag to compile .F90 files... none
configure: determining Fortran module case
checking whether Fortran modules are upper-case... no
checking how to get verbose linking output from /home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort... -v
checking for Fortran libraries of /home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort... -L/home/sana/intel/Compiler/11.1/073/mkl/lib/32 -L/home/sana/intel/Compiler/11.1/073/lib/ia32 -L/home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/lib/ia32 -L/usr/lib/gcc/i486-linux-gnu/4.4.3/ -L/usr/lib/gcc/i486-linux-gnu/4.4.3/../../../../lib/ -L/lib/../lib/ -L/usr/lib/../lib/ -L/usr/lib/gcc/i486-linux-gnu/4.4.3/../../../ -L/lib/ -L/usr/lib/ -L/usr/lib/i486-linux-gnu -lifport -lifcore -limf -lsvml -lm -lipgo -lirc -lirc_s -ldl
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
==============================================================================
=== Python support ===
==============================================================================
checking for python... python
checking for python-config... no
checking for python2.6-config... no
checking for python2.5-config... no
checking for python2.4-config... no
checking for Python CPPFLAGS...
checking for bzr... no
checking for Python NumPy headers... not found
checking numarray/arrayobject.h usability... no
checking numarray/arrayobject.h presence... no
checking for numarray/arrayobject.h... no
==============================================================================
=== Libraries and linking ===
==============================================================================
checking for ar... ar
checking for ranlib... ranlib
==============================================================================
=== Hints ===
==============================================================================
checking for cpp... cpp
checking for a true C preprocessor... cpp
checking which cpp hints to apply... default/default/default
checking which cc hints to apply... gnu/default/default
checking which xpp hints to apply... none/none/none
checking which cxx hints to apply... gnu/default/default
checking which fpp hints to apply... default/default/default
checking which fc hints to apply... intel/default/default
checking which ar hints to apply... none/none/none
checking which Fortran preprocessor to use...
checking which Fortran preprocessor flags to apply...
checking whether to wrap Fortran compiler calls... no
==============================================================================
=== Debugging ===
==============================================================================
checking debugging status... enabled (using compiler defaults)
configure: setting C debug flags to '-g'
configure: setting C++ debug flags to '-g'
configure: setting Fortran debug flags to '-g'
checking whether to activate debug mode in source files... no
checking whether to activate design-by-contract debugging... no
==============================================================================
=== Optimizations ===
==============================================================================
checking optimization status... enabled (profile mode: standard)
checking which cc optimizations to apply... gnu/default/default
checking which cxx optimizations to apply... gnu/default/default
checking which fc optimizations to apply... intel/default/default
checking whether to apply per-directory optimizations... yes
==============================================================================
=== 64-bit support ===
==============================================================================
checking for a 64-bit architecture... no
checking whether to use 64-bit flags... no
checking for user-defined 64-bit flags...
==============================================================================
=== Build flags ===
==============================================================================
configure: static builds may be performed
==============================================================================
=== Advanced compiler features ===
==============================================================================
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking mcheck.h usability... yes
checking mcheck.h presence... yes
checking for mcheck.h... yes
checking for abort... yes
checking size of char... 1
checking size of short... 2
checking size of int... 4
checking size of long... 4
checking size of long long... 8
checking size of unsigned int... 4
checking size of unsigned long... 4
checking size of unsigned long long... 8
checking size of float... 4
checking size of double... 8
checking size of long double... 12
checking size of size_t... 4
checking size of ptrdiff_t... 4
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether the Fortran compiler provides the iso_c_binding module... yes
checking whether the Fortran compiler accepts exit()... yes
checking whether the Fortran compiler accepts flush()... no
checking whether the Fortran compiler accepts flush_()... no
checking whether the Fortran compiler accepts gamma()... no
checking whether the Fortran compiler accepts getenv()... no
checking whether the Fortran compiler accepts getpid()... no
checking whether the Fortran compiler accepts the null() intrinsic... yes
checking whether the Fortran compiler accepts quadruple integers... no
checking whether the Fortran compiler accepts long lines... no
checking whether the Fortran compiler accepts etime()... no
checking whether to use C clock for timings... no
==============================================================================
=== Connectors ===
==============================================================================
checking whether MPI is usable... no
configure: WARNING: MPI support is broken!
checking whether to build MPI code... yes
checking whether to build MPI I/O code... yes
checking whether to build MPI I/O untested features... no
checking whether to build MPI time tracing code... no
checking which level of MPI is supported by the Fortran compiler... none
checking whether to activate GPU support... no
checking whether to use transferable I/O libraries... no
checking whether to use optimized timer libraries... no
checking whether to use optimized linear algebra libraries... yes
checking whether to activate ScaLAPACK support... no
checking for the requested linear algebra support... netlib
checking for zgemm in -lblas... no
checking for zhpev in -llapack... no
checking for the actual linear algebra support... none
checking whether to use optimized math libraries... no
checking whether to use optimized FFT libraries... no
checking whether to use DFT libraries... no
==============================================================================
=== Plug-ins ===
==============================================================================
configure: using tarball repository /home/sana/.abinit/tarballs
checking whether to enable the FOX plug-in... no
checking whether to build the FOX plug-in... no
checking for a source tarball of NETCDF... yes
configure: WARNING: tarball MD5 check failed
configure: downloading NETCDF - this may take a while
configure: WARNING: tarball MD5 check failed
configure: WARNING: could not download NETCDF plug-in tarball
configure: WARNING: support for NETCDF plug-in has been disabled
checking whether to enable the NETCDF plug-in... no
checking whether to build the NETCDF plug-in... no
checking whether to enable the ETSF_IO plug-in... no
checking whether to build the ETSF_IO plug-in... no
checking for a source tarball of LIBXC... no
configure: downloading LIBXC - this may take a while
checking availability of LIBXC from URL 1... configure: WARNING: could not download LIBXC plug-in tarball
configure: WARNING: support for LIBXC plug-in has been disabled
no
checking whether to enable the LIBXC plug-in... no
checking whether to build the LIBXC plug-in... no
checking whether to enable the BIGDFT plug-in... no
checking whether to build the BIGDFT plug-in... no
checking for a source tarball of WANNIER90... yes
configure: tarball MD5 check succeeded
configure: applying Wannier90 tricks (vendor: intel, version: 11.1)
checking whether to enable the WANNIER90 plug-in... yes
checking whether to build the WANNIER90 plug-in... yes
==============================================================================
=== Nightly builds ===
==============================================================================
checking whether to build test timeout code... no
checking timeout for automatic tests... none
==============================================================================
=== Experimental developments ===
==============================================================================
checking whether to enable bindings... no
checking whether to enable BSE unpacking... no
checking whether to enable CLib... no
checking whether to build exports... no
checking whether to accelerate 'make check'... no
checking whether to enable GW cut-off... no
checking whether to enable GW double-precision calculations... no
checking whether to enable optimal GW... no
checking whether to enable GW wrapper... no
checking whether to activate maintainer checks... no
checking whether to use macroave... yes
checking whether to read input from stdin... yes
checking whether to activate Symmetric Multi-Processing... no
checking whether to activate ZDOTC and ZDOTU workaround... no
==============================================================================
=== Output ===
==============================================================================
configure: creating ./config.status
config.status: creating config.dump
config.status: creating config.mk
config.status: creating config.pc
config.status: creating config.sh
config.status: creating config/wrappers/wrap-fc
config.status: creating src/incs/Makefile
config.status: creating src/mods/Makefile
config.status: creating src/16_hideleave/m_build_info.F90
config.status: creating tests/tests.env
config.status: creating tests/tests-install.env
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/01_gsl_ext/Makefile
config.status: creating src/01_interfaces_ext/Makefile
config.status: creating src/01_macroavnew_ext/Makefile
config.status: creating src/01_qespresso_ext/Makefile
config.status: creating src/02_clib/Makefile
config.status: creating src/10_defs/Makefile
config.status: creating src/12_hide_mpi/Makefile
config.status: creating src/14_hidewrite/Makefile
config.status: creating src/15_gpu_toolbox/Makefile
config.status: creating src/16_hideleave/Makefile
config.status: creating src/18_timing/Makefile
config.status: creating src/27_toolbox_oop/Makefile
config.status: creating src/28_numeric_noabirule/Makefile
config.status: creating src/32_contract/Makefile
config.status: creating src/32_util/Makefile
config.status: creating src/42_geometry/Makefile
config.status: creating src/42_geomoptim/Makefile
config.status: creating src/42_nlstrain/Makefile
config.status: creating src/42_parser/Makefile
config.status: creating src/43_ptgroups/Makefile
config.status: creating src/45_psp_parser/Makefile
config.status: creating src/47_xml/Makefile
config.status: creating src/49_gw_toolbox_oop/Makefile
config.status: creating src/50_abitypes_defs/Makefile
config.status: creating src/51_manage_cuda/Makefile
config.status: creating src/51_manage_mpi/Makefile
config.status: creating src/52_fft_mpi_noabirule/Makefile
config.status: creating src/53_abiutil/Makefile
config.status: creating src/53_ffts/Makefile
config.status: creating src/53_spacepar/Makefile
config.status: creating src/56_recipspace/Makefile
config.status: creating src/56_xc/Makefile
config.status: creating src/57_iovars/Makefile
config.status: creating src/59_io_mpi/Makefile
config.status: creating src/61_ionetcdf/Makefile
config.status: creating src/62_cg_noabirule/Makefile
config.status: creating src/62_iowfdenpot/Makefile
config.status: creating src/62_occeig/Makefile
config.status: creating src/62_poisson/Makefile
config.status: creating src/62_wvl_wfs/Makefile
config.status: creating src/63_bader/Makefile
config.status: creating src/64_atompaw/Makefile
config.status: creating src/65_nonlocal/Makefile
config.status: creating src/65_psp/Makefile
config.status: creating src/66_paw/Makefile
config.status: creating src/66_wfs/Makefile
config.status: creating src/67_common/Makefile
config.status: creating src/68_dmft/Makefile
config.status: creating src/68_gw/Makefile
config.status: creating src/68_recursion/Makefile
config.status: creating src/68_rsprc/Makefile
config.status: creating src/69_bse/Makefile
config.status: creating src/72_response/Makefile
config.status: creating src/77_ddb/Makefile
config.status: creating src/77_lwf/Makefile
config.status: creating src/77_suscep/Makefile
config.status: creating src/79_seqpar_mpi/Makefile
config.status: creating src/83_cut3d/Makefile
config.status: creating src/93_rdm/Makefile
config.status: creating src/95_drive/Makefile
config.status: creating src/98_main/Makefile
config.status: creating src/libs/Makefile
config.status: creating tests/Nightly/Makefile
config.status: creating prereqs/Makefile
config.status: creating prereqs/linalg/Makefile
config.status: creating plugins/Makefile
config.status: creating plugins/bigdft/Makefile
config.status: creating plugins/etsf_io/Makefile
config.status: creating plugins/fox/Makefile
config.status: creating plugins/libxc/Makefile
config.status: creating plugins/netcdf/Makefile
config.status: creating plugins/wannier90/Makefile
config.status: creating bindings/Makefile
config.status: creating bindings/parser/Makefile
config.status: creating doc/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing dump-optim commands
config.status: executing script-perms commands
config.status: executing long-lines commands
+--------------------------------------------------------------+
| About the Intel Fortran compiler |
+--------------------------------------------------------------+
| Your compiler will work properly only if the LD_LIBRARY_PATH |
| and INTEL_LICENSE_FILE environment variables are correctly |
| set-up. Please make sure that this is the case before |
| building ABINIT. |
| |
| In most cases it means sourcing a script in the Intel |
| compiler install directory, e.g.: |
| |
| . /opt/intel/fc/9.1/bin/ifortvars.sh |
| |
| for a Bourne-like shell (do not forget the leading dot), or |
| |
| source /opt/intel/fc/9.1/bin/ifortvars.csh |
| |
| for a C-like shell. |
| |
| If you do not know what this is all about, please refer to |
| the Intel documentation or ask your system administrator. |
| |
| Please note that the same holds for the Intel C and C++ |
| compilers. |
+--------------------------------------------------------------+
Configuration complete.
You may now type "make" to build ABINIT.
(or, on a SMP machine, "make mj4", or "make multi multi_nprocs=<n>")
sana@sana-desktop:~/Desktop/abinit-6.2.2_impi4.0$ make |tee make.log
make all-recursive
make[1]: Entering directory `/home/sana/Desktop/abinit-6.2.2_impi4.0'
Making all in prereqs
make[2]: Entering directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/prereqs'
Making all in linalg
make[3]: Entering directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/prereqs/linalg'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/prereqs/linalg'
make[3]: Entering directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/prereqs'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/prereqs'
make[2]: Leaving directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/prereqs'
Making all in plugins
make[2]: Entering directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/plugins'
Making all in wannier90
make[3]: Entering directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/plugins/wannier90'
make -f ../../plugins/wannier90/wannier90.mk
make[4]: Entering directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/plugins/wannier90'
gzip -cd /home/sana/.abinit/tarballs/wannier90-1.2.tar.gz | tar xf -
cd wannier90-1.2 && patch -p1 < /home/sana/Desktop/abinit-6.2.2_impi4.0/plugins/wannier90/wannier90-1.2-0001.patch
patching file src/disentangle.F90
patching file src/overlap.F90
patching file src/parameters.F90
patching file src/plot.F90
patching file src/wannier_lib.F90
cd wannier90-1.2 && patch -p1 < /home/sana/Desktop/abinit-6.2.2_impi4.0/plugins/wannier90/wannier90-1.2-0002.patch
patching file src/transport.F90
touch uncompress-stamp
wannier90-1.2 has been uncompressed.
mkdir tmp
echo "F90 = /home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort" > wannier90-1.2/make.sys
echo "FCOPTS = -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O3 -xHost" >> wannier90-1.2/make.sys
echo "LDOPTS = -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O3 -xHost -static-intel -static-libgcc " >> wannier90-1.2/make.sys
echo "LIBS = -L/home/sana/Desktop/abinit-6.2.2_impi4.0/prereqs/linalg -llapack -lblas -L/home/sana/Desktop/abinit-6.2.2_impi4.0/prereqs/linalg -llapack -lblas -lsvml" >> wannier90-1.2/make.sys
touch configure-stamp
wannier90-1.2 has been configured.
cd wannier90-1.2 && make wannier lib
make[5]: Entering directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/plugins/wannier90/wannier90-1.2'
(cd src ; make prog)
make[6]: Entering directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/plugins/wannier90/wannier90-1.2/src'
/home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O3 -xHost -c constants.F90
/home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O3 -xHost -c io.F90
/home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O3 -xHost -c utility.F90
/home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O3 -xHost -c parameters.F90
/home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O3 -xHost -c hamiltonian.F90
/home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O3 -xHost -c overlap.F90
/home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O3 -xHost -c kmesh.F90
/home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O3 -xHost -c disentangle.F90
/home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O3 -xHost -c wannierise.F90
/home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O3 -xHost -c plot.F90
/home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O3 -xHost -c transport.F90
/home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/bin/ia32/ifort wannier_prog.F90 -free -g -extend-source -vec-report0 -noaltparam -nofpscomp -O3 -xHost -static-intel -static-libgcc constants.o io.o utility.o parameters.o hamiltonian.o overlap.o kmesh.o disentangle.o wannierise.o plot.o transport.o -L/home/sana/Desktop/abinit-6.2.2_impi4.0/prereqs/linalg -llapack -lblas -L/home/sana/Desktop/abinit-6.2.2_impi4.0/prereqs/linalg -llapack -lblas -lsvml -o ../wannier90.x
ld: ../wannier90.x: hidden symbol `__intel_cpu_indicator_init' in /home/sana/Desktop/Compilers-MPI/intel/Compiler/11.1/073/lib/ia32/libirc.a(cpu_disp.o) is referenced by DSO
ld: final link failed: Nonrepresentable section on output
make[6]: *** [prog] Error 1
make[6]: Leaving directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/plugins/wannier90/wannier90-1.2/src'
make[5]: *** [wannier] Error 2
make[5]: Leaving directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/plugins/wannier90/wannier90-1.2'
make[4]: *** [build-stamp] Error 2
make[4]: Leaving directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/plugins/wannier90'
make[3]: *** [package-ready] Error 2
make[3]: Leaving directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/plugins/wannier90'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/sana/Desktop/abinit-6.2.2_impi4.0/plugins'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/sana/Desktop/abinit-6.2.2_impi4.0'
make: *** [all] Error 2